How can I fix this scaling issue I have?
I think your mesh is not aligned with its own object's local axes.. (you may have reoriented the cube in Edit Mode). So the Local axes are aligned to Global axes, but the mesh isn't, it wouldn't make any difference whether you transform in Local or Global. It's probably quickest to start with a new cube. 

But you could select its top face, and CtrlAltSpace create a Custom Orientation from it, checking 'Use after Creation' and then transform the object in that space, SXX,SYY, etc. 

You could even reoirient the cube's local axes to one of its faces, by snapping a helper cube to one of its faces,CtrlJ, joining the object to the helper, and deleting the helper in Edit Mode.. but in this case, that would be silly.